Can You Really Sequence DNA With a USB Thumb Drive?

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Can You Really Sequence DNA With a USB Thumb Drive?

Nigel Chapman

What if you could put a few bacterial cells into a USB stick, plug it into your laptop, and get back a complete DNA sequence in a matter of minutes?

Oxford Nanopore has built a USB device that will do just that. At least, that's what the company says. Known as MinION, the device received a hefty amount of press when it was announced in February, and it's slated for release to the world at large in the second half of the year. But many are still skeptical that this tiny device will do what it's designed to do.

"If [the claims] are true, we'd buy it tomorrow," Jonathan Eisen, a microbiology professor at the University of California at Davis. "But I'm reserving judgment. We've heard many presentations from companies where these things don't pan out."

Clive Brown, Oxford's chief technology officer, tells Wired that the MinION works as advertised. You put a handful of lysed cells – cells whose membranes have been dissolved – into a small container built into the USB drive. You plug the drive into an ordinary PC. And depending on the length of the DNA in those cells, you'll have a complete sequence in somewhere between a few minutes to a few hours. The device – which is used once and discarded – is the result of seven years of research, Brown says, and it sells for $900.

For Eisen, the cost alone would make the MinION a game changer. But it's also attractive because it's portable. Eisen says that with a device like the MinION, field researchers would have sequencing at their fingertips at all times, whether they're on a remote mountain somewhere or out at sea looking at algae blooms. "This really would be the democratization of sequencing," he says. "Anyone in any research environment would consider doing large scale sequencing in their project."

But he still wants to see it action before he says any more.

In biological research, the order of DNA's four building blocks – called base pairs – is essential to understanding the underlying mechanisms of an organism's existence. Short for deoxyribonucleic acid, DNA – along with a handful of supporting molecules – dictates the protein structures and development of every creature on the planet. DNA length varies by organism – ranging from the thousands of basepairs for bacteria to billions for mammals – so tools that quickly read this molecular instruction manual are imperative for biological research.

The market for DNA sequencing is a crowded one. Companies such as Sequetech outsource the service, Illumina builds large machines that sit alongside a lab bench, and Ion Torrent, a subsidiary of Life Technologies, will soon release a benchtop sequencer that it says will read the entire human genome – roughly three billion base pairs – in a day. But Oxford is the first to put this sort of device on an ordinary laptop.

The company does this using "nanopores" – i.e. very small holes. Researchers take a biological sample and inject it into the USB stick. DNA from the sample then passes through hundreds of those tiny holes, and as it does so, electrical sensors read the DNA base pairs as they pass by.

Each base pair has a slightly different shape and charge and generates a different signal for the sensor, and these signals are fed into a specialized processor – known as an ASIC (application specific integrated circuit) – that sits right on the nanopores. Oxford partnered with a Defense Department contractor in San Diego to build this chip, but it won't say who this partner was. The trick is that the chip can process information from the nanopores in parallel. There's a circuit for each nanopore.

According to Clive Brown, Oxford's chief technology officer, the process is kind of like a game of Hungry Hippo. After a researcher inserts a DNA sample, each nanopore gobbles up it up as fast as they can, independent of the nanopore next door. Brown says that today, each nanopore is sending about 33,000 measurements per second. The first version of MinION will have a single ASIC chip with 512 circuits and 512 nanopores, but he says they will likely add a second chip to the next iteration.

The advantage to this parallel processing of DNA is that the bioinformatics – the actual analysis of the order and concentration of the DNA – can be done in real-time. Other DNA sequencers work slightly differently, identifying one base at a time, but the MinION measures large chunks simultaneously, so that a full picture of entire swaths of DNA can form all at once. If you're looking for a particular gene, you can stop running the analysis when it shows up, rather than waiting for the whole sequence.

In many cases, researchers take DNA samples that have a great deal of "noise" or contaminant DNA. Whether you're taking samples from pond water or the railing on the subway, there is always extra DNA floating around that blurs the sequence you're actually looking for. Contaminant noise is one factor to account for, but a second comes directly from the sensor itself, since measuring the tickertape of bases passing by is not a perfect science yet. But according to Brown, a tiny field-programmable gate array alleviates some of that noise, reducing it by a factor of about 100.

The data then flows out via USB to a computer, where Oxford's custom application takes the digital fragments of DNA and pieces them back together into a useable sequence. Oxford partnered with a software company called Accelrys to rework the company's visual workflow builder, Pipeline Pilot, for use with DNA sequencing. With Pipeline Pilot, you feed data into a series of programmable algorithms, and it spits back an analysis. Oxford and Accelrys took the myriad libraries of bioinformatics algorithms that exist in the public domain and plugged them into Pipeline Pilot.

Different labs use different bioinformatics principles, so the ability to reorder the different tools is needed. This also allows other researchers to replicate your work, so they can see exactly what you did – each run is exportable in an XML file – and then do it themselves.

Oxford sees the device being used by just a single researcher, eliminating the need to buy big equipment or hire staff that understand the nitty gritty of bioinformatics. "You leverage existing IT infrastructure," Gordon Sanghera, Oxford Nanopore's CEO says. "You don't need to spend half a million dollars on an instrument."

Greg Lucier – the CEO of Life Technologies, a competitor in the DNA sequencing games – tells Wired that while his company researches nanopore technology, he does not think it's a practical way to handle DNA sequencing because it can't provide the sort of accuracy you get from larger systems. "There is no way a standard computer could do that kind of processing," he says.

We'll know for sure later this year.

[Updated: We updated this story to clarify the sensor and noise reduction mechanisms of the nanopore device. Sequetech's business model was clarified. "Pipeline" was changed to "Pipeline Pilot".]